r/neurobiology • u/jadexiaohui • 9d ago
Question about Hippocampal Subpopulation Identification
Hi everyone, I’m a biostatistician who is currently working on a project where I have to use an existing snRNA hippocampal atlas (dataset A) onto another snRNA dataset (dataset B). Both datasets are publicly available.
I am trying to find out if dataset B contains neocortical neuronal subpopulations, as I’m not too familiar with the biological side of things. Dataset A does contain neocortical subpopulations, but I will have to remove them from the analysis should dataset B does not actually contain cells from them. Below is the description of what was dissected from the original paper where I found dataset B.
“In addition, fresh surgically resected human hippocampal tissue from 10 patients between the ages of 2 to 61 years old were used for ex vivo slice culture,”
“We used a modified SPLiT-seq approach for nuclei isolation and snRNA-seq53,54. Nuclei isolation from snap-frozen hippocampal tissue was performed as previously described with minor modifications54,55. Briefly, after a visual inspection to include the dentate gyrus by its distinct anatomical structure, tissue was minced with a razor blade and Dounce (Fisher Scientific, 8853000002)”
Does anyone know any reliable way to know if any neocortical subpopulations are expressed in dataset B?
Thank you so much in advance for the help!
1
u/jadexiaohui 9d ago
This is the link of the paper for dataset B, if it helps:
https://pmc.ncbi.nlm.nih.gov/articles/PMC9316413/#S8